Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009574.1 Hibiscus syriacus cultivar Beakdansim tig00116939_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2686660
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 14
Found at i:1722965 original size:21 final size:21
Alignment explanation
Indices: 1722901--1723001 Score: 103
Period size: 21 Copynumber: 4.8 Consensus size: 21
1722891 TGATATATTA
* * *
1722901 CTTCTCTCTGTTCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* * *
1722922 CCTCTCTCTGTGCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
1722943 CTTCTCTCTCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* **
1722964 CTGCTCTAGCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* *
1722985 CTGCTCTCTCTGTTTCC
1 CTTCTCTCTCTGCTTCC
1723002 TTTGCTTCAT
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 69 1.00
ACGTcount: A:0.01, C:0.41, G:0.19, T:0.40
Consensus pattern (21 bp):
CTTCTCTCTCTGCTTCCGCTG
Found at i:1731077 original size:21 final size:21
Alignment explanation
Indices: 1731051--1731090 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1731041 CGAAACATCA
1731051 TTCGTGTTCAGTAAAAAACAT
1 TTCGTGTTCAGTAAAAAACAT
1731072 TTCGTGTTCAGTAAAAAAC
1 TTCGTGTTCAGTAAAAAAC
1731091 TAATTGCTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (21 bp):
TTCGTGTTCAGTAAAAAACAT
Found at i:1731855 original size:42 final size:42
Alignment explanation
Indices: 1731809--1731947 Score: 120
Period size: 42 Copynumber: 3.3 Consensus size: 42
1731799 ATGTGTAATA
*
1731809 TATTGCGGCGTTTTTTGTCAAAACGCCGCCAATTTACCACTC
1 TATTGCGGCGTTTTTAGTCAAAACGCCGCCAATTTACCACTC
* * * * * *
1731851 TATTGCAGCGTTTTGACTC-AATCGCCGCAAAATTTA-TACTC
1 TATTGCGGCGTTTTTAGTCAAAACGCCGC-CAATTTACCACTC
* * * * * * *
1731892 TATTGTGGCGTTTGTGGTAAAAACGCTGCCAGTTTACCACTA
1 TATTGCGGCGTTTTTAGTCAAAACGCCGCCAATTTACCACTC
*
1731934 TATTGTGGCGTTTT
1 TATTGCGGCGTTTT
1731948 GGCTAAATCG
Statistics
Matches: 73, Mismatches: 21, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
41 29 0.40
42 44 0.60
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (42 bp):
TATTGCGGCGTTTTTAGTCAAAACGCCGCCAATTTACCACTC
Found at i:1731903 original size:41 final size:40
Alignment explanation
Indices: 1731847--1731979 Score: 115
Period size: 41 Copynumber: 3.2 Consensus size: 40
1731837 CCAATTTACC
** *
1731847 ACTCTATTGCAGCGTTTTGACTCAATCGCCGCAAAATTTAT
1 ACTCTATTGTGGCGTTTTG-CTAAATCGCCGCAAAATTTAT
* * * * * *
1731888 ACTCTATTGTGGCGTTTGTGGTAAAAACGCTGC-CAGTTTACC
1 ACTCTATTGTGGCGTTT-TGCT-AAATCGCCGCAAAATTTA-T
*
1731930 ACTATATTGTGGCGTTTTGGCTAAATCGCCGCAAAATTTAT
1 ACTCTATTGTGGCGTTTT-GCTAAATCGCCGCAAAATTTAT
*
1731971 AATCTATTG
1 ACTCTATTG
1731980 AAGCGTTTGT
Statistics
Matches: 69, Mismatches: 18, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
41 37 0.54
42 32 0.46
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (40 bp):
ACTCTATTGTGGCGTTTTGCTAAATCGCCGCAAAATTTAT
Found at i:1731928 original size:83 final size:83
Alignment explanation
Indices: 1731804--1732010 Score: 252
Period size: 83 Copynumber: 2.5 Consensus size: 83
1731794 ACTATATGTG
* * * * * *
1731804 TAATATATTGCGGCGTTTTTTGTCAAAACGCCGCCAATTTACCACTCTATTGCAGCGTTTTGACT
1 TAATCTATTGAGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTATATTGCAGCGTTTTGACT
*
1731869 CAATCGCCGCAAAATTTA
66 AAATCGCCGCAAAATTTA
* * * * ** *
1731887 TACTCTATTGTGGCGTTTGTGGTAAAAACGCTGCCAGTTTACCACTATATTGTGGCGTTTTGGCT
1 TAATCTATTGAGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTATATTGCAGCGTTTTGACT
1731952 AAATCGCCGCAAAATTTA
66 AAATCGCCGCAAAATTTA
* * * *
1731970 TAATCTATTGAAGCGTTTGTGATATAAACGCCGCTAATTTA
1 TAATCTATTGAGGCGTTTGTGGTAAAAACGCCGCCAATTTA
1732011 GCACCCTATT
Statistics
Matches: 103, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
83 103 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (83 bp):
TAATCTATTGAGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTATATTGCAGCGTTTTGACT
AAATCGCCGCAAAATTTA
Found at i:1732027 original size:83 final size:83
Alignment explanation
Indices: 1731828--1732030 Score: 262
Period size: 83 Copynumber: 2.4 Consensus size: 83
1731818 GTTTTTTGTC
* * *
1731828 AAAACGCCGCCAATTTACCACTCTATTGCAGCGTTTTGACTCAATCGCCGCAAAATTTATACTCT
1 AAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTTGACTAAATCGCCGCAAAATTTATAATCT
** *
1731893 ATTGTGGCGTTTGTGGTA
66 ATTGAAGCGTTTGTGATA
* * * * *
1731911 AAAACGCTGCCAGTTTACCACTATATTGTGGCGTTTTGGCTAAATCGCCGCAAAATTTATAATCT
1 AAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTTGACTAAATCGCCGCAAAATTTATAATCT
1731976 ATTGAAGCGTTTGTGATA
66 ATTGAAGCGTTTGTGATA
* * * * *
1731994 TAAACGCCGCTAATTTAGCACCCTATTACGGCGTTTT
1 AAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTT
1732031 TCTAAAAACG
Statistics
Matches: 100, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
83 100 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (83 bp):
AAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTTGACTAAATCGCCGCAAAATTTATAATCT
ATTGAAGCGTTTGTGATA
Found at i:1739609 original size:44 final size:44
Alignment explanation
Indices: 1739536--1739699 Score: 202
Period size: 44 Copynumber: 3.7 Consensus size: 44
1739526 GAGATTTAGA
* * * ** *
1739536 GGCATTTTTTGGATACAAATGTCAATAAAGGTCTTGTATATAGC
1 GGCATTTTTAGGATACAAACGCCGCTAAAGGTCTAGTATATAGC
* ** * *
1739580 CGTGTTTTTAGGATGCAAACGCCGCTAAAGATCTAGTATATAGC
1 GGCATTTTTAGGATACAAACGCCGCTAAAGGTCTAGTATATAGC
* *
1739624 GGCATTTTTAAGATACAAACGCCGCTAAAGGTCTGGTATATAGC
1 GGCATTTTTAGGATACAAACGCCGCTAAAGGTCTAGTATATAGC
*
1739668 GGCATTTTTAGTATACAAACGCCGCTAAAGGT
1 GGCATTTTTAGGATACAAACGCCGCTAAAGGT
1739700 TTATAAATAA
Statistics
Matches: 100, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 100 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (44 bp):
GGCATTTTTAGGATACAAACGCCGCTAAAGGTCTAGTATATAGC
Found at i:1745576 original size:43 final size:43
Alignment explanation
Indices: 1745529--1745620 Score: 98
Period size: 42 Copynumber: 2.1 Consensus size: 43
1745519 AATGGCGTTT
* * **
1745529 TAATGTTAA-AAACATTTACGGTGTTTTTTTGTCAAAACGCCAC
1 TAATGTTAAGAAACATTTACGGCG-TTTGTTACCAAAACGCCAC
* *
1745572 TAATG-TAAGAATCATTTGCGGCGTTTGTTACCAAAACGCCAC
1 TAATGTTAAGAAACATTTACGGCGTTTGTTACCAAAACGCCAC
1745614 TATATGT
1 TA-ATGT
1745621 GAACCCTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
42 21 0.52
43 19 0.47
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (43 bp):
TAATGTTAAGAAACATTTACGGCGTTTGTTACCAAAACGCCAC
Found at i:1745732 original size:190 final size:187
Alignment explanation
Indices: 1745373--1745803 Score: 555
Period size: 190 Copynumber: 2.3 Consensus size: 187
1745363 TTTTAATTAT
* * * * *
1745373 AAACGCAACTAATGTAAAAAACATTTGCGGCATTTGTTACCAAAACGCCGCTATATGTGAACCCT
1 AAACGCCACTAATGTAAGAATCATTTGCGGCGTTTGTTACCAAAACGCCACTATATGTGAACCCT
* *
1745438 ATACAACGTTTTTTTCAAAACGCCGCTAAAGTACTAATTTGTTACGGCGTTTATTAAAAACGCCG
66 ATAC-ACGTTTTTTTCAAAACGCCGCTAAAGTACTAATATGTTACGGCGTATATTAAAAACGCCG
* * *
1745503 CTATATATCTAAAGTTAATGGCGTTTTAATGTTAAAAACATTTACGGTGTTTTTTTGTCA
130 CTATATATCTAAAGTTAATGGCGTTTTAATATAAAAAACATTTACGGCG--TTTTTGTCA
1745563 AAACGCCACTAATGTAAGAATCATTTGCGGCGTTTGTTACCAAAACGCCACTATATGTGAACCCT
1 AAACGCCACTAATGTAAGAATCATTTGCGGCGTTTGTTACCAAAACGCCACTATATGTGAACCCT
* * *
1745628 ATTGC-GGTATTTTTGTCAAAACGCCGCTAAAGTACTAATATGTTACGGCGTATATTAAAAAATG
66 A-TACACGT-TTTTT-TCAAAACGCCGCTAAAGTACTAATATGTTACGGCGTATATT-AAAAACG
* * * *
1745692 TCGTTATATGTCTAAAGTTAATGGCG-TTTAA-ATAAAAAACATTTGCGGCGTTTTTGTCA
127 CCGCTATATATCTAAAGTTAATGGCGTTTTAATATAAAAAACATTTACGGCGTTTTTGTCA
* * * * * *
1745751 AAACGACACTAAAT-TATGAATTATTTACGACGTTTGTTACCAAAACGCTACTA
1 AAACGCCACT-AATGTAAGAATCATTTGCGGCGTTTGTTACCAAAACGCCACTA
1745804 AAACAAACGA
Statistics
Matches: 213, Mismatches: 23, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
188 52 0.24
189 5 0.02
190 81 0.38
191 46 0.22
192 29 0.14
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (187 bp):
AAACGCCACTAATGTAAGAATCATTTGCGGCGTTTGTTACCAAAACGCCACTATATGTGAACCCT
ATACACGTTTTTTTCAAAACGCCGCTAAAGTACTAATATGTTACGGCGTATATTAAAAACGCCGC
TATATATCTAAAGTTAATGGCGTTTTAATATAAAAAACATTTACGGCGTTTTTGTCA
Found at i:1747662 original size:82 final size:81
Alignment explanation
Indices: 1747562--1747721 Score: 196
Period size: 83 Copynumber: 2.0 Consensus size: 81
1747552 CACTATTACT
* * * * *
1747562 ACTCTATAGCGGTGTTTGT-ATAAAAACGCCGCTAAATGACTACTCTTTTGTGGCATTTGTTGAT
1 ACTCTATACCGGTGTTTGTCAT-AAAACGCCGCTAAATGACCACTCTATTGCGGCATTTGTTG-G
1747626 AAAACGCCACTATAAATA
64 AAAACGCCACTATAAATA
* * * *
1747644 ACTCTATACCGGTGTTTGTGCCTTAAACGCCGCTAAATTACCACTCTATTGCGGCATTTTTTGGA
1 ACTCTATACCGGTGTTTGT-CATAAAACGCCGCTAAATGACCACTCTATTGCGGCATTTGTTGGA
*
1747709 AAACGCCGCTATA
65 AAACGCCACTATA
1747722 TTATCATTTG
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
82 31 0.47
83 34 0.52
84 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (81 bp):
ACTCTATACCGGTGTTTGTCATAAAACGCCGCTAAATGACCACTCTATTGCGGCATTTGTTGGAA
AACGCCACTATAAATA
Found at i:1748525 original size:18 final size:18
Alignment explanation
Indices: 1748471--1748530 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
1748461 CTATTTTGAT
1748471 TTTTTATTAT-TTGTATTA
1 TTTTTATTATATT-TATTA
* *
1748489 TTATTATTATCACCATTATTA
1 TTTTTATTAT-A--TTTATTA
1748510 TTTTTATTATATTTATTA
1 TTTTTATTATATTTATTA
1748528 TTT
1 TTT
1748531 AGGGTTTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 18 0.53
20 1 0.03
21 14 0.41
22 1 0.03
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTTATTATATTTATTA
Found at i:1753301 original size:2 final size:2
Alignment explanation
Indices: 1753294--1753329 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1753284 ATTTGGTAAG
1753294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1753330 CCTTCAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1756189 original size:24 final size:24
Alignment explanation
Indices: 1756159--1756208 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1756149 TAAATAAGAA
1756159 AATAATTTTCTCAATCCTTTATAT
1 AATAATTTTCTCAATCCTTTATAT
1756183 AATAATTTTCTCAATCCTTTATAT
1 AATAATTTTCTCAATCCTTTATAT
1756207 AA
1 AA
1756209 GTAAATCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (24 bp):
AATAATTTTCTCAATCCTTTATAT
Found at i:1766829 original size:55 final size:55
Alignment explanation
Indices: 1766632--1766829 Score: 252
Period size: 55 Copynumber: 3.6 Consensus size: 55
1766622 TGTATGAGTG
* * * *
1766632 TGTATCGGTACACTTAGGAGTGTATCGATACCTTCAAAACATCAAATGCCATTTA
1 TGTATCAGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGCCATTTA
* * * * *
1766687 TGTATCAGTATACTGAGGAGTGTATTGATACACTCAAAACATTGAATGCCATCTA
1 TGTATCAGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGCCATTTA
* * * * ** *
1766742 TGTTTCGGTACACTAAGGAGTGTATCGATACCCTCAAAACATCGAGTGTTATTTG
1 TGTATCAGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGCCATTTA
1766797 TGTATCAGTACACTGAGGAGTGTATCGATACCC
1 TGTATCAGTACACTGAGGAGTGTATCGATACCC
1766830 CCAAGTATGA
Statistics
Matches: 119, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 119 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (55 bp):
TGTATCAGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGCCATTTA
Found at i:1767363 original size:21 final size:21
Alignment explanation
Indices: 1767339--1767385 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1767329 TTCGAGGATC
* * *
1767339 TATGTGGTCCTTCGGGATAAT
1 TATGTGGTCCTCCGGGACAAA
1767360 TATGTGGTCCTCCGGGACAAA
1 TATGTGGTCCTCCGGGACAAA
1767381 TATGT
1 TATGT
1767386 TGCACTTCGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (21 bp):
TATGTGGTCCTCCGGGACAAA
Found at i:1767415 original size:23 final size:22
Alignment explanation
Indices: 1767389--1767440 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1767379 AATATGTTGC
* *
1767389 ACTTCGGTGCAACCCTATGTGGT
1 ACTTCGGTACAA-CCTATGTAGT
*
1767412 ACTTCAGTACAACCTATGTAGT
1 ACTTCGGTACAACCTATGTAGT
*
1767434 CCTTCGG
1 ACTTCGG
1767441 GATAATTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (22 bp):
ACTTCGGTACAACCTATGTAGT
Found at i:1773447 original size:55 final size:53
Alignment explanation
Indices: 1773371--1773570 Score: 283
Period size: 55 Copynumber: 3.7 Consensus size: 53
1773361 TTTGTATGAG
* * *
1773371 TGTGTATCGGTATACTTAGGAGTGTATCGATACCCTAAAAACATCGAATGTAATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATC-AATGT-ATT
*
1773426 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAAGATCAAATGTCATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATC-AATGT-ATT
*
1773481 TCTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCAAGTGCTATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCAA-TG-TATT
* *
1773536 TTTGTATTGGTACACTGAGGAGTGTATCGATACCC
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACCC
1773571 CCAAGTATGA
Statistics
Matches: 133, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
54 2 0.02
55 130 0.98
56 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.31
Consensus pattern (53 bp):
TGTGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCAATGTATT
Found at i:1773566 original size:110 final size:110
Alignment explanation
Indices: 1773373--1773570 Score: 319
Period size: 110 Copynumber: 1.8 Consensus size: 110
1773363 TGTATGAGTG
* *
1773373 TGTATCGGTATACTTAGGAGTGTATCGATACCCTAAAAACATCGAATGTAATTTGTGTATCGGTA
1 TGTATCGGTACACTGAGGAGTGTATCGATACCCTAAAAACATCGAATGTAATTTGTGTATCGGTA
1773438 CACTGAGGAGTGTATCGATACCCTCAAAAGATCAAATGTCATTTC
66 CACTGAGGAGTGTATCGATACCCTCAAAAGATCAAATGTCATTTC
* * *
1773483 TGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATC-AAGTGCT-ATTTTTGTATTGG
1 TGTATCGGTACACTGAGGAGTGTATCGATACCCTAAAAACATCGAA-TG-TAATTTGTGTATCGG
1773546 TACACTGAGGAGTGTATCGATACCC
64 TACACTGAGGAGTGTATCGATACCC
1773571 CCAAGTATGA
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
109 2 0.02
110 78 0.96
111 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (110 bp):
TGTATCGGTACACTGAGGAGTGTATCGATACCCTAAAAACATCGAATGTAATTTGTGTATCGGTA
CACTGAGGAGTGTATCGATACCCTCAAAAGATCAAATGTCATTTC
Found at i:1774730 original size:15 final size:15
Alignment explanation
Indices: 1774707--1774814 Score: 180
Period size: 15 Copynumber: 7.2 Consensus size: 15
1774697 CGTAGGACTC
1774707 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
1774722 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
1774737 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
1774752 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
1774767 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
1774782 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
*
1774797 TTACATCCCGAAGGA
1 CTACATCCCGAAGGA
1774812 CTA
1 CTA
1774815 TTATACCCTC
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 85 1.00
ACGTcount: A:0.31, C:0.32, G:0.22, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:1774743 original size:30 final size:30
Alignment explanation
Indices: 1774707--1774814 Score: 207
Period size: 30 Copynumber: 3.6 Consensus size: 30
1774697 CGTAGGACTC
1774707 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
1774737 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
1774767 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
*
1774797 TTACATCCCGAAGGACTA
1 CTACATCCCGAAGGACTA
1774815 TTATACCCTC
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 77 1.00
ACGTcount: A:0.31, C:0.32, G:0.22, T:0.15
Consensus pattern (30 bp):
CTACATCCCGAAGGACTACGTCCCGAAGGA
Found at i:1774941 original size:29 final size:29
Alignment explanation
Indices: 1774899--1774976 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
1774889 TTTCATATGT
1774899 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1774927 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1774956 TCATGTAGCTCATGTCATTTC
1 TCATGTAGCTCATGTCATTTC
1774977 ATATCATGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.14
29 42 0.86
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1775015 original size:12 final size:12
Alignment explanation
Indices: 1774988--1775034 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
1774978 TATCATGTTC
**
1774988 TCATATCACAGG
1 TCATATCACATA
1775000 TCATATCACATA
1 TCATATCACATA
*
1775012 TCATACCACATA
1 TCATATCACATA
*
1775024 GCATATCACAT
1 TCATATCACAT
1775035 GAACATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.38, C:0.28, G:0.06, T:0.28
Consensus pattern (12 bp):
TCATATCACATA
Found at i:1775436 original size:64 final size:64
Alignment explanation
Indices: 1775328--1775504 Score: 214
Period size: 64 Copynumber: 2.8 Consensus size: 64
1775318 AATTTCCGGT
* * * ** * * **
1775328 ATGCATCGATGCACTACTGATGCATCGGTGCA-TCAAAGGTATTCGATGTAGTATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-GATTGCATTCGATGTAGTACTATTAATGGG
* **
1775392 ATGCATCGATGCACTCCTTATGCATCGATGCACTGATTGCATTCGATGTTTTACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTGATTGCATTCGATGTAGTACTATTAATGGG
1775456 ATGCATCGATGCACTACTTATGCATCGATGCAC-GAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACTG-ATTGCATTCGATGT
1775505 CTTTATTTCA
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
63 1 0.01
64 96 0.98
65 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTGATTGCATTCGATGTAGTACTATTAATGGG
Found at i:1775552 original size:65 final size:64
Alignment explanation
Indices: 1775391--1775553 Score: 190
Period size: 64 Copynumber: 2.5 Consensus size: 64
1775381 TTATTGTTGG
** *
1775391 GATGCATCGATGCACT-CCTTATGCATCGATGCACTGATTGCATTCGATGTTTTACTATTAATGG
1 GATGCATCGATGCACTACC-TATGCATCGATGCACTGATTGCATTCGATGTTTTACTAAAAATGA
* *
1775455 GATGCATCGATGCACTACTTATGCATCGATGCAC-GAATTGCATTCGATGTCTTTATTTCAAAAA
1 GATGCATCGATGCACTACCTATGCATCGATGCACTG-ATTGCATTCGATGT-TTTA-CT-AAAAA
1775519 T-A
62 TGA
* *
1775521 G-TGCATCGATGCACTACCAATGCGTCGATGCAC
1 GATGCATCGATGCACTACCTATGCATCGATGCAC
1775554 ATTCATATAA
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 45 0.52
65 34 0.40
66 2 0.02
67 4 0.05
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (64 bp):
GATGCATCGATGCACTACCTATGCATCGATGCACTGATTGCATTCGATGTTTTACTAAAAATGA
Found at i:1781740 original size:15 final size:15
Alignment explanation
Indices: 1781717--1781794 Score: 138
Period size: 15 Copynumber: 5.2 Consensus size: 15
1781707 CGTAGGACTC
*
1781717 CTACATCCCGAAGGA
1 CTACGTCCCGAAGGA
1781732 CTACGTCCCGAAGGA
1 CTACGTCCCGAAGGA
1781747 CTACGTCCCGAAGGA
1 CTACGTCCCGAAGGA
1781762 CTACGTCCCGAAGGA
1 CTACGTCCCGAAGGA
*
1781777 CTACATCCCGAAGGA
1 CTACGTCCCGAAGGA
1781792 CTA
1 CTA
1781795 TTATACCCTC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 61 1.00
ACGTcount: A:0.29, C:0.33, G:0.23, T:0.14
Consensus pattern (15 bp):
CTACGTCCCGAAGGA
Found at i:1781922 original size:29 final size:29
Alignment explanation
Indices: 1781880--1781957 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
1781870 TTTCATATGT
1781880 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1781908 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1781937 TCATGTAGCTCATGTCATTTC
1 TCATGTAGCTCATGTCATTTC
1781958 ATATCATGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.14
29 42 0.86
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1781996 original size:12 final size:12
Alignment explanation
Indices: 1781969--1782015 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
1781959 TATCATGTTC
**
1781969 TCATATCACAGG
1 TCATATCACATA
1781981 TCATATCACATA
1 TCATATCACATA
*
1781993 TCATACCACATA
1 TCATATCACATA
*
1782005 GCATATCACAT
1 TCATATCACAT
1782016 GAACATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.38, C:0.28, G:0.06, T:0.28
Consensus pattern (12 bp):
TCATATCACATA
Found at i:1782432 original size:64 final size:63
Alignment explanation
Indices: 1782324--1782500 Score: 219
Period size: 64 Copynumber: 2.8 Consensus size: 63
1782314 TAATGAAGGT
* * * ** * * **
1782324 ATGCATCGATGCACTACTGATGCATCGGTGCATCAAAGGTATTCGATGTAGTATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTAGTACTATTAATGGG
* **
1782388 ATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTTACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTAGTACTATTAATGGG
1782452 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATGT
1782501 CTTTATTTCA
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
63 2 0.02
64 96 0.98
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTAGTACTATTAATGGG
Found at i:1782548 original size:65 final size:63
Alignment explanation
Indices: 1782387--1782549 Score: 197
Period size: 64 Copynumber: 2.5 Consensus size: 63
1782377 TTATTGTTGG
** *
1782387 GATGCATCGATGCACT-CCTTATGCATCGATGCACCGATTGCATTCGATGTTTTACTATTAATGG
1 GATGCATCGATGCACTACC-TATGCATCGATGCA-CGATTGCATTCGATGTTTTACTAAAAATGA
* *
1782451 GATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTATTTCAAAAAT
1 GATGCATCGATGCACTACCTATGCATCGATGCACG-ATTGCATTCGATGT-TTTA-CT-AAAAAT
1782516 -A
62 GA
*
1782517 G-TGCATCGATGCACTACCAATGCATCGATGCAC
1 GATGCATCGATGCACTACCTATGCATCGATGCAC
1782550 ATTCATATAA
Statistics
Matches: 87, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 2 0.02
64 44 0.51
65 35 0.40
66 2 0.02
67 4 0.05
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (63 bp):
GATGCATCGATGCACTACCTATGCATCGATGCACGATTGCATTCGATGTTTTACTAAAAATGA
Found at i:1783387 original size:21 final size:20
Alignment explanation
Indices: 1783361--1783410 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
1783351 AGTCGAGGGT
1783361 TTATGTGGTCCTTCGGAATAA
1 TTATGTGGTCCTTCGGAA-AA
*
1783382 TTATGTGGTCCTCCGGGAAAA
1 TTATGTGGTCCTTC-GGAAAA
*
1783403 ATATGTGG
1 TTATGTGG
1783411 CACTTCGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (20 bp):
TTATGTGGTCCTTCGGAAAA
Found at i:1783434 original size:23 final size:23
Alignment explanation
Indices: 1783404--1783478 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
1783394 CCGGGAAAAA
1783404 TATGTGGCACTTCGGTGCAACCC
1 TATGTGGCACTTCGGTGCAACCC
* * *
1783427 TATGTGGCACTTCGATGTAACCA
1 TATGTGGCACTTCGGTGCAACCC
*
1783450 TATGTGGCACTTAGGTGCAA-CC
1 TATGTGGCACTTCGGTGCAACCC
1783472 TATGTGG
1 TATGTGG
1783479 TTCTTCGAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 8 0.18
23 37 0.82
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAACCC
Found at i:1783455 original size:46 final size:42
Alignment explanation
Indices: 1783402--1783512 Score: 132
Period size: 46 Copynumber: 2.5 Consensus size: 42
1783392 CTCCGGGAAA
1783402 AATATGTGGCACTTCGGTGCAACCCTATGTGGCACTTCGATGTAAC
1 AATATGTGGCACTTCGGTGCAA-CCTATGTGGCACTTCGA-G--AC
* * **
1783448 CATATGTGGCACTTAGGTGCAACCTATGTGGTTCTTCGAGAC
1 AATATGTGGCACTTCGGTGCAACCTATGTGGCACTTCGAGAC
*
1783490 AATTATGTGGTACTTCGGTGCAA
1 AA-TATGTGGCACTTCGGTGCAA
1783513 ATTATGAGCT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
42 3 0.05
43 18 0.32
44 1 0.02
45 15 0.26
46 20 0.35
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (42 bp):
AATATGTGGCACTTCGGTGCAACCTATGTGGCACTTCGAGAC
Found at i:1799281 original size:12 final size:13
Alignment explanation
Indices: 1799254--1799292 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
1799244 TGTCTATGAG
1799254 ATAATATTTATTT
1 ATAATATTTATTT
1799267 ATAATATTT-TTT
1 ATAATATTTATTT
*
1799279 ATAAGATTATATTT
1 ATAATATT-TATTT
1799293 CTTAACCGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 10 0.43
13 10 0.43
14 3 0.13
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
ATAATATTTATTT
Found at i:1799964 original size:2 final size:2
Alignment explanation
Indices: 1799957--1799981 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1799947 GGGCCAGAAA
1799957 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1799982 GAGCATCTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1800151 original size:2 final size:2
Alignment explanation
Indices: 1800144--1800189 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1800134 ATTCTAACCC
1800144 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1800186 TA TA
1 TA TA
1800190 GAATAGTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1802213 original size:21 final size:23
Alignment explanation
Indices: 1802185--1802243 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 23
1802175 TGTTGGATTT
1802185 TTAA-ATTTATTATTAT-T-ATTA
1 TTAATATTTATT-TTATATAATTA
1802206 TT-ATATTT-TTTTATATAATTA
1 TTAATATTTATTTTATATAATTA
*
1802227 TTAATATTTAATTTATA
1 TTAATATTTATTTTATA
1802244 ATACACAGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 12 0.38
22 6 0.19
23 6 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTAATATTTATTTTATATAATTA
Found at i:1803875 original size:23 final size:22
Alignment explanation
Indices: 1803820--1803882 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
1803810 GATTTTTTTA
* * *
1803820 TGAATAGTGATGAACAATATCG
1 TGAACAGTGATGAACAGTACCG
* *
1803842 TAAACAATGATGAACAGTACCCG
1 TGAACAGTGATGAACAGTA-CCG
1803865 TGAACAGTGATGAACAGT
1 TGAACAGTGATGAACAGT
1803883 GTATCGATGC
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.22
Consensus pattern (22 bp):
TGAACAGTGATGAACAGTACCG
Found at i:1803980 original size:12 final size:12
Alignment explanation
Indices: 1803957--1804003 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
1803947 GCATCGATGC
*
1803957 ACTGCTATAGTA
1 ACTGCTACAGTA
*
1803969 ACTGCTGCAGT-
1 ACTGCTACAGTA
* *
1803980 ACTACTACAATA
1 ACTGCTACAGTA
1803992 ACTGCTACAGTA
1 ACTGCTACAGTA
1804004 TTTTCAACAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
11 8 0.30
12 19 0.70
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (12 bp):
ACTGCTACAGTA
Found at i:1804563 original size:33 final size:33
Alignment explanation
Indices: 1804526--1804624 Score: 198
Period size: 33 Copynumber: 3.0 Consensus size: 33
1804516 TCGTAGTGCC
1804526 AATCCGTATGACACATAAGGTCGTGTCCACCAT
1 AATCCGTATGACACATAAGGTCGTGTCCACCAT
1804559 AATCCGTATGACACATAAGGTCGTGTCCACCAT
1 AATCCGTATGACACATAAGGTCGTGTCCACCAT
1804592 AATCCGTATGACACATAAGGTCGTGTCCACCAT
1 AATCCGTATGACACATAAGGTCGTGTCCACCAT
1804625 CTGTACTAGG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (33 bp):
AATCCGTATGACACATAAGGTCGTGTCCACCAT
Found at i:1807114 original size:20 final size:20
Alignment explanation
Indices: 1807089--1807127 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1807079 TTGCTATTTT
1807089 AAAAAAAAAAACAAAAAAAG
1 AAAAAAAAAAACAAAAAAAG
**
1807109 AAAAAAAAAGCCAAAAAAA
1 AAAAAAAAAAACAAAAAAA
1807128 AAGCCAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAACAAAAAAAG
Found at i:1807127 original size:23 final size:23
Alignment explanation
Indices: 1807101--1807147 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1807091 AAAAAAAAAC
1807101 AAAAAAAG-AAAAAAAAAGCCAA
1 AAAAAAAGCAAAAAAAAAGCCAA
*
1807123 AAAAAAAGCCAAAAAAAAGCCAA
1 AAAAAAAGCAAAAAAAAAGCCAA
1807146 AA
1 AA
1807148 TTTCAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.79, C:0.13, G:0.09, T:0.00
Consensus pattern (23 bp):
AAAAAAAGCAAAAAAAAAGCCAA
Found at i:1807141 original size:11 final size:11
Alignment explanation
Indices: 1807101--1807147 Score: 69
Period size: 11 Copynumber: 4.3 Consensus size: 11
1807091 AAAAAAAAAC
*
1807101 AAAAAAAG-AA
1 AAAAAAAGCCA
1807111 AAAAAAAGCCAA
1 AAAAAAAGCC-A
1807123 AAAAAAAGCCA
1 AAAAAAAGCCA
1807134 AAAAAAAGCCA
1 AAAAAAAGCCA
1807145 AAA
1 AAA
1807148 TTTCAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
10 8 0.24
11 15 0.44
12 11 0.32
ACGTcount: A:0.79, C:0.13, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAGCCA
Found at i:1808298 original size:55 final size:55
Alignment explanation
Indices: 1808214--1808459 Score: 350
Period size: 55 Copynumber: 4.5 Consensus size: 55
1808204 TATATGTTGC
* * * *
1808214 AATTTCTGTATTGGCACTATGTGTGCAACCCTATAAAATTCATAATGAATTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
* * *
1808269 AATTTCCGTATTGACACTATGTGCGCAACCTCAC-AAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
*
1808323 AATTTTCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
* * * *
1808378 AATTTCCATATTGACACTATGTGTACAACCCCACGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
** *
1808433 AATTTTTGTATTGGCACTATATGTGCA
1 AATTTCCGTATTGGCACTATGTGTGCA
1808460 TGTAACATCC
Statistics
Matches: 168, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
54 49 0.29
55 119 0.71
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (55 bp):
AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
Found at i:1808407 original size:109 final size:110
Alignment explanation
Indices: 1808216--1808459 Score: 391
Period size: 109 Copynumber: 2.2 Consensus size: 110
1808206 TATGTTGCAA
* * *
1808216 TTTCTGTATTGGCACTATGTGTGCAACCCTATAAAATTCATAATGAATTTATGAATTTCCGTATT
1 TTTC-GTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAATTTATGAATTTCCATATT
* *
1808281 GACACTATGTGCGCAACCTCAC-AAATTCATAATGAGTTTATGAAT
65 GACACTATGTGCACAACCCCACGAAATTCATAATGAGTTTATGAAT
*
1808326 TTTCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATGAATTTCCATATTG
1 TTTCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAATTTATGAATTTCCATATTG
*
1808391 ACACTATGTGTACAACCCCACGAAATTCATAATGAGTTTATGAAT
66 ACACTATGTGCACAACCCCACGAAATTCATAATGAGTTTATGAAT
* *
1808436 TTTTGTATTGGCACTATATGTGCA
1 TTTCGTATTGGCACTATGTGTGCA
1808460 TGTAACATCC
Statistics
Matches: 124, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
109 75 0.60
110 49 0.40
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (110 bp):
TTTCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAATTTATGAATTTCCATATTG
ACACTATGTGCACAACCCCACGAAATTCATAATGAGTTTATGAAT
Found at i:1810441 original size:2 final size:2
Alignment explanation
Indices: 1810434--1810468 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
1810424 ATAAGTTTTC
*
1810434 AT AT AT AT AT AT AT AT AT AT AT GT AT AT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
1810469 GTTAATATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1810880 original size:18 final size:18
Alignment explanation
Indices: 1810854--1810890 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1810844 GTTCTTAAGG
*
1810854 AGTGGTCATTCGGGACAT
1 AGTGATCATTCGGGACAT
*
1810872 AGTGATCATTTGGGACAT
1 AGTGATCATTCGGGACAT
1810890 A
1 A
1810891 TGTGTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.30
Consensus pattern (18 bp):
AGTGATCATTCGGGACAT
Found at i:1811766 original size:55 final size:55
Alignment explanation
Indices: 1811682--1811873 Score: 235
Period size: 55 Copynumber: 3.5 Consensus size: 55
1811672 GGTGTTACAA
*
1811682 TGCAACCCCACAAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTG
1 TGCAACCCCACGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTG
* * *
1811737 TGCAACCCCACGTAATTCATAATGAGTTTATGAATTAT-CGTATTGACACAATGTG
1 TGCAACCCCACGAAATTCATAATGAGTTTATGAATT-TCCGTATTGGCACTATGTG
* * * ** *
1811792 TGC-ACCCCACGTAATTCATAATGAGTTTGTGAATTACCAAATTGGCAATATGTG
1 TGCAACCCCACGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTG
** * *
1811846 TGCAAAACCATGAAATTTATAATGAGTT
1 TGCAACCCCACGAAATTCATAATGAGTT
1811874 AATATATTGA
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
54 46 0.39
55 71 0.60
56 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (55 bp):
TGCAACCCCACGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTG
Found at i:1811845 original size:54 final size:54
Alignment explanation
Indices: 1811686--1811849 Score: 222
Period size: 54 Copynumber: 3.0 Consensus size: 54
1811676 TTACAATGCA
** * *
1811686 ACCCCACAAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTGC
1 ACCCCACGTAATTCATAATGAGTTTATGAATTACCGTATTGGCAATATGTGTGC
* *
1811740 AACCCCACGTAATTCATAATGAGTTTATGAATTATCGTATTGACACA-ATGTGTGC
1 -ACCCCACGTAATTCATAATGAGTTTATGAATTACCGTATTGGCA-ATATGTGTGC
* **
1811795 ACCCCACGTAATTCATAATGAGTTTGTGAATTACCAAATTGGCAATATGTGTGC
1 ACCCCACGTAATTCATAATGAGTTTATGAATTACCGTATTGGCAATATGTGTGC
1811849 A
1 A
1811850 AAACCATGAA
Statistics
Matches: 96, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
53 1 0.01
54 48 0.50
55 47 0.49
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (54 bp):
ACCCCACGTAATTCATAATGAGTTTATGAATTACCGTATTGGCAATATGTGTGC
Found at i:1812239 original size:2 final size:2
Alignment explanation
Indices: 1812232--1812262 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1812222 AATGTGTTTA
1812232 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1812263 ATTGAAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1815672 original size:24 final size:24
Alignment explanation
Indices: 1815640--1815711 Score: 135
Period size: 24 Copynumber: 3.0 Consensus size: 24
1815630 AGTCTTCCTG
1815640 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
1815664 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
*
1815688 ATGATGTATAAAACGTCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
1815712 CATGTCATGC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:1816288 original size:31 final size:30
Alignment explanation
Indices: 1816253--1816321 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
1816243 AATTCACAAT
* *
1816253 TTTTCTAAAATTACTAAATTGGTCCCCTAAC
1 TTTTCTAAAATTA-TAAAATGGTCCCCAAAC
* *
1816284 TTTTCAAAAATTATAAAATGGTCCCCAAAT
1 TTTTCTAAAATTATAAAATGGTCCCCAAAC
1816314 TTTTCTAA
1 TTTTCTAA
1816322 GGCTTGTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 21 0.64
31 12 0.36
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (30 bp):
TTTTCTAAAATTATAAAATGGTCCCCAAAC
Found at i:1820421 original size:55 final size:55
Alignment explanation
Indices: 1820337--1820687 Score: 517
Period size: 55 Copynumber: 6.4 Consensus size: 55
1820327 TATATGTTTC
* * *
1820337 AATTTCCGTATTGGCACTATGTGTGCAACCCCACTAAATTAATAATGAGTTTATT
1 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
* * * *
1820392 AATTTCCGTATTGGCACTATGTATGCAACCCTAAAAAATTCATAATGATTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
*
1820447 AATTTCCGTATT-ACACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
1820501 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
** *
1820556 AATTTCCGTATTGGCACTATGTGTGCAACCCCACGTAATTTATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
* *** * *
1820611 AATTACCGTATTGGCACTATGTGTGC-ACCCCATGTAATTGATAATGAGTTTGTG
1 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
* *
1820665 AATTACCGTATCGGCACTATGTG
1 AATTTCCGTATTGGCACTATGTG
1820688 CTCAAAACCA
Statistics
Matches: 274, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
54 96 0.35
55 178 0.65
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (55 bp):
AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
Found at i:1820478 original size:109 final size:110
Alignment explanation
Indices: 1820337--1820687 Score: 519
Period size: 109 Copynumber: 3.2 Consensus size: 110
1820327 TATATGTTTC
*
1820337 AATTTCCGTATTGGCACTATGTGTGCAACCCCACTAAATTAATAATGAGTTTATTAATTTCCGTA
1 AATTTCCGTATTGGCACTATGTGTGCAACCCCACTAAATTAATAATGAGTTTATGAATTTCCGTA
* * *
1820402 TTGGCACTATGTATGCAACCCTAAAAAATTCATAATGATTTTATG
66 TTGGCACTATGTGTGCAACCCCAAAAAATTCATAATGAGTTTATG
* * *
1820447 AATTTCCGTATT-ACACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATGAATTTCCGTA
1 AATTTCCGTATTGGCACTATGTGTGCAACCCCACTAAATTAATAATGAGTTTATGAATTTCCGTA
*
1820511 TTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
66 TTGGCACTATGTGTGCAACCCCAAAAAATTCATAATGAGTTTATG
* *
1820556 AATTTCCGTATTGGCACTATGTGTGCAACCCCACGT-AATTTATAATGAGTTTATGAATTACCGT
1 AATTTCCGTATTGGCACTATGTGTGCAACCCCAC-TAAATTAATAATGAGTTTATGAATTTCCGT
*** * *
1820620 ATTGGCACTATGTGTGC-ACCCCATGTAATTGATAATGAGTTTGTG
65 ATTGGCACTATGTGTGCAACCCCAAAAAATTCATAATGAGTTTATG
* *
1820665 AATTACCGTATCGGCACTATGTG
1 AATTTCCGTATTGGCACTATGTG
1820688 CTCAAAACCA
Statistics
Matches: 220, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
109 145 0.66
110 75 0.34
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (110 bp):
AATTTCCGTATTGGCACTATGTGTGCAACCCCACTAAATTAATAATGAGTTTATGAATTTCCGTA
TTGGCACTATGTGTGCAACCCCAAAAAATTCATAATGAGTTTATG
Found at i:1820611 original size:164 final size:164
Alignment explanation
Indices: 1820337--1820687 Score: 515
Period size: 164 Copynumber: 2.1 Consensus size: 164
1820327 TATATGTTTC
* *
1820337 AATTTCCGTATTGGCACTATGTGTGCAACCCCACTAAATTAATAATGAGTTTATTAATTTCCGTA
1 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTAATAATGAGTTTATGAATTTCCGTA
* * *
1820402 TTGGCACTATGTATGCAACCCTAAAAAATTCATAATGATTTTATGAATTTCCGTATT-ACACTAT
66 TTGGCACTATGTATGCAACCCCAAAAAATTCATAATGAGTTTATGAATTACCGTATTGACACTAT
1820466 GTGTGCAACCCCACAAAATTCATAATGAGTTTATG
131 GTGTGC-ACCCCACAAAATTCATAATGAGTTTATG
*
1820501 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATGAATTTCCGTA
1 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTAATAATGAGTTTATGAATTTCCGTA
* *** * *
1820566 TTGGCACTATGTGTGCAACCCCACGTAATTTATAATGAGTTTATGAATTACCGTATTGGCACTAT
66 TTGGCACTATGTATGCAACCCCAAAAAATTCATAATGAGTTTATGAATTACCGTATTGACACTAT
*** * *
1820631 GTGTGCACCCCATGTAATTGATAATGAGTTTGTG
131 GTGTGCACCCCACAAAATTCATAATGAGTTTATG
* *
1820665 AATTACCGTATCGGCACTATGTG
1 AATTTCCGTATTGGCACTATGTG
1820688 CTCAAAACCA
Statistics
Matches: 167, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
164 155 0.93
165 12 0.07
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (164 bp):
AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTAATAATGAGTTTATGAATTTCCGTA
TTGGCACTATGTATGCAACCCCAAAAAATTCATAATGAGTTTATGAATTACCGTATTGACACTAT
GTGTGCACCCCACAAAATTCATAATGAGTTTATG
Found at i:1821542 original size:15 final size:15
Alignment explanation
Indices: 1821522--1821563 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
1821512 ATTCCTCTAG
1821522 TATTGATATCAAAGA
1 TATTGATATCAAAGA
1821537 TATTGATATCAAAGA
1 TATTGATATCAAAGA
*
1821552 TATTGGTATCAA
1 TATTGATATCAA
1821564 CATTAGGCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (15 bp):
TATTGATATCAAAGA
Found at i:1824227 original size:21 final size:22
Alignment explanation
Indices: 1824202--1824260 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
1824192 GCATTCAAAG
*
1824202 GGTATCGATACCTGGGAAGGTA
1 GGTATCGATACCTGGGAAGGGA
*
1824224 -GTATCGATACCT--TAAGGGA
1 GGTATCGATACCTGGGAAGGGA
*
1824243 GGTATCGATACCAGGGAA
1 GGTATCGATACCTGGGAA
1824261 ATATCGAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 5 0.17
20 11 0.37
21 12 0.40
22 2 0.07
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.22
Consensus pattern (22 bp):
GGTATCGATACCTGGGAAGGGA
Found at i:1824780 original size:24 final size:24
Alignment explanation
Indices: 1824752--1824810 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
1824742 ATGTGAAATA
1824752 ATGAAAGTGATCA-TATGTGTGCAT
1 ATGAAAGTGAT-ATTATGTGTGCAT
* *
1824776 GTG-AAGTGA-ATTATGTGTTCAT
1 ATGAAAGTGATATTATGTGTGCAT
1824798 ATGAGAAGTGATA
1 ATGA-AAGTGATA
1824811 AAAGAGATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 1 0.04
22 12 0.43
23 6 0.21
24 8 0.29
25 1 0.04
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (24 bp):
ATGAAAGTGATATTATGTGTGCAT
Found at i:1833523 original size:24 final size:24
Alignment explanation
Indices: 1833496--1833543 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1833486 CTCAATTTCA
1833496 TTTATCACCATCATGCATTTTATG
1 TTTATCACCATCATGCATTTTATG
*
1833520 TTTATCATCATCATGCATTTTATG
1 TTTATCACCATCATGCATTTTATG
1833544 AATGTCATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (24 bp):
TTTATCACCATCATGCATTTTATG
Found at i:1833551 original size:24 final size:24
Alignment explanation
Indices: 1833498--1833558 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
1833488 CAATTTCATT
* **
1833498 TATCACCATCATGCATTTTATGTT
1 TATCATCATCATGCATTTTATGAA
1833522 TATCATCATCATGCATTTTATGAA
1 TATCATCATCATGCATTTTATGAA
* *
1833546 TGTCATGATCATG
1 TATCATCATCATG
1833559 TTTATGCCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.43
Consensus pattern (24 bp):
TATCATCATCATGCATTTTATGAA
Found at i:1834543 original size:11 final size:11
Alignment explanation
Indices: 1834517--1834550 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1834507 TCTTGAACCC
*
1834517 CTTTTATTTATT
1 CTTTT-TTTTTT
1834529 CTTTTTTTTTT
1 CTTTTTTTTTT
1834540 CTTTTTTTTTT
1 CTTTTTTTTTT
1834551 TCATTTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:1834545 original size:12 final size:12
Alignment explanation
Indices: 1834517--1834567 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
1834507 TCTTGAACCC
*
1834517 CTTTTATTTATT
1 CTTTTATTTTTT
1834529 CTTTT-TTTTTT
1 CTTTTATTTTTT
*
1834540 CTTTTTTTTTTT
1 CTTTTATTTTTT
*
1834552 CATTTCATTTTTT
1 C-TTTTATTTTTT
1834565 CTT
1 CTT
1834568 ATTCTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.29
12 14 0.41
13 10 0.29
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (12 bp):
CTTTTATTTTTT
Found at i:1834562 original size:25 final size:25
Alignment explanation
Indices: 1834534--1834607 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 25
1834524 TTATTCTTTT
*
1834534 TTTTTTCTT-TTTTTTTTTCATTTC
1 TTTTTTCTTATTTTTTTTTCACTTC
*
1834558 ATTTTTTCTTATTCTTTTATTCACTTC
1 -TTTTTTCTTATT-TTTTTTTCACTTC
*
1834585 TTCTTCTTCTTCTTTTTTCTTTC
1 TT-TT-TTCTTATTTTTT-TTTC
1834608 TTTAGGCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 9 0.22
26 4 0.10
27 17 0.43
28 10 0.25
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTTTCTTATTTTTTTTTCACTTC
Found at i:1843408 original size:22 final size:23
Alignment explanation
Indices: 1843378--1843432 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
1843368 CAGACAGAAT
* *
1843378 CGATACCCCC-TTGAAGGGGAAC
1 CGATTCCCCCTTTGAAGGGAAAC
1843400 CGATTCCCCCTTTGAAGGGAAAC
1 CGATTCCCCCTTTGAAGGGAAAC
1843423 CGATTCCCCC
1 CGATTCCCCC
1843433 CCACAGGGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 9 0.30
23 21 0.70
ACGTcount: A:0.24, C:0.36, G:0.22, T:0.18
Consensus pattern (23 bp):
CGATTCCCCCTTTGAAGGGAAAC
Found at i:1845046 original size:18 final size:18
Alignment explanation
Indices: 1845023--1845061 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1845013 GGAGCAGCAC
*
1845023 GAGGAACAACCTCCTCCA
1 GAGGAACAACCTCATCCA
1845041 GAGGAACAACCTCATCCA
1 GAGGAACAACCTCATCCA
1845059 GAG
1 GAG
1845062 TATCAAATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.33, G:0.21, T:0.10
Consensus pattern (18 bp):
GAGGAACAACCTCATCCA
Found at i:1853303 original size:65 final size:64
Alignment explanation
Indices: 1853165--1853290 Score: 148
Period size: 65 Copynumber: 2.0 Consensus size: 64
1853155 AACAAGCCAG
* * * * *
1853165 AGTGCATCGATGCATAAAATGCATTTGATGTTTTCATAAATCCCTGAGTGTATCGATGCATGCT
1 AGTGCATCGAAGCATAAAATGCATTAGATGTTTTAATAAATCACTGAGTGCATCGATGCATGCT
* * *
1853229 ATGTGCATCGAAGCATAAAATGCATTAGATG-TTTAAGTTATTCATTG-GTGCATCGATGCATG
1 A-GTGCATCGAAGCATAAAATGCATTAGATGTTTTAA-TAAATCACTGAGTGCATCGATGCATG
1853291 GATTAGTGCA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
64 19 0.37
65 33 0.63
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (64 bp):
AGTGCATCGAAGCATAAAATGCATTAGATGTTTTAATAAATCACTGAGTGCATCGATGCATGCT
Found at i:1853786 original size:17 final size:17
Alignment explanation
Indices: 1853764--1853797 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1853754 GATCAAAGAT
1853764 CAAGAGAAAGGTTAGCC
1 CAAGAGAAAGGTTAGCC
1853781 CAAGAGAAAGGTTAGCC
1 CAAGAGAAAGGTTAGCC
1853798 ATTAGTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.29, T:0.12
Consensus pattern (17 bp):
CAAGAGAAAGGTTAGCC
Found at i:1855756 original size:23 final size:22
Alignment explanation
Indices: 1855726--1855804 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
1855716 GCATGGTAGT
1855726 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
1855748 AGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
1855770 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
1855793 GATGCATCGATG
1 G-TGCATCGATG
1855805 TACTGTTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 19 0.42
24 9 0.20
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:1855782 original size:21 final size:22
Alignment explanation
Indices: 1855726--1855788 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
1855716 GCATGGTAGT
1855726 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTC-AGGA
* * *
1855749 GTGCATCGGTGCACCTTCATG-
1 GTGCATCGATGCACATTCAGGA
*
1855770 GTGTATCGATGCACATTCA
1 GTGCATCGATGCACATTCA
1855789 AAGGGATGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 16 0.47
22 2 0.06
23 16 0.47
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGA
Found at i:1861690 original size:65 final size:64
Alignment explanation
Indices: 1861567--1861724 Score: 189
Period size: 65 Copynumber: 2.5 Consensus size: 64
1861557 CACTAAGAGT
* *
1861567 GCATCGATG-A-AAGAAGTGCATTCGATGTTTCAAACAAGCCAGAGTGCATCGATGCATGGTCTG
1 GCATCGATGCATAA-AA-TGCATTCGATGTTTCAAACAAGCCAGAGTGCATCGATACATGGTATG
1861630 C
64 C
* *
1861631 GCATCGATGCATAAAATGCATTCGATGATTTCATAA-AA-CCTTGAGTGTATCGATACATGGTAT
1 GCATCGATGCATAAAATGCATTCGATG-TTTCA-AACAAGCC-AGAGTGCATCGATACATGGTAT
*
1861694 GT
63 GC
*
1861696 GCATCAATGCATAAAATGCATTCGATGTT
1 GCATCGATGCATAAAATGCATTCGATGTT
1861725 CAATTTATTC
Statistics
Matches: 83, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
64 24 0.29
65 55 0.66
66 4 0.05
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (64 bp):
GCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGCCAGAGTGCATCGATACATGGTATGC
Found at i:1869094 original size:3 final size:3
Alignment explanation
Indices: 1869086--1869117 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1869076 ACTACATCAT
1869086 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1869118 GGTCATGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1872017 original size:3 final size:3
Alignment explanation
Indices: 1872009--1872034 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1871999 TAAAGTTTTG
1872009 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1872035 ATATCCTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1873432 original size:26 final size:26
Alignment explanation
Indices: 1873403--1873455 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1873393 CCGAAATACC
1873403 AATACACATAAGGTCGTGCCCACCAT
1 AATACACATAAGGTCGTGCCCACCAT
*
1873429 AATACATATAAGGTCGTGCCCACCAT
1 AATACACATAAGGTCGTGCCCACCAT
1873455 A
1 A
1873456 TGCATTAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (26 bp):
AATACACATAAGGTCGTGCCCACCAT
Found at i:1878808 original size:21 final size:21
Alignment explanation
Indices: 1878764--1878821 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
1878754 TTTTGGTGCA
* *
1878764 GAAGGAATCGA-TCCCCCCTT
1 GAAGGAACCGATTCCACCCTT
*
1878784 GAAGGAACCGATTCCACCTTT
1 GAAGGAACCGATTCCACCCTT
1878805 GAAGGGGAACCGATTCC
1 GAA--GGAACCGATTCC
1878822 CCCCCACAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.31
21 10 0.31
23 12 0.38
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (21 bp):
GAAGGAACCGATTCCACCCTT
Found at i:1893109 original size:25 final size:24
Alignment explanation
Indices: 1893072--1893140 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 24
1893062 GTCCCTGTCC
*
1893072 CCGTCCCCGTTTAAAAAATTCATA
1 CCGTCCCCGTTTAAAAAACTCATA
*
1893096 TCCGTCCCCATTTAAAAAACTCATA
1 -CCGTCCCCGTTTAAAAAACTCATA
*
1893121 CTCGTCCCCGCTTAAAAAAC
1 C-CGTCCCCGTTTAAAAAAC
1893141 CGCGGGGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 1 0.03
25 38 0.97
ACGTcount: A:0.33, C:0.33, G:0.07, T:0.26
Consensus pattern (24 bp):
CCGTCCCCGTTTAAAAAACTCATA
Found at i:1893312 original size:32 final size:33
Alignment explanation
Indices: 1893247--1893329 Score: 105
Period size: 38 Copynumber: 2.4 Consensus size: 33
1893237 TCGGGCCGGC
1893247 TATATATATAT-TTAAATTAAATATATAAATAT
1 TATATATATATATTAAATTAAATATATAAATAT
*
1893279 TATATATATATATTAAATTAAATTAAATTTATTAATAT
1 TATATATATATATTAAATTAAA-T--A--TATAAATAT
1893317 TATATATATATAT
1 TATATATATATAT
1893330 ATAATAATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
32 11 0.25
33 10 0.23
34 1 0.02
36 1 0.02
38 21 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
TATATATATATATTAAATTAAATATATAAATAT
Found at i:1896104 original size:31 final size:31
Alignment explanation
Indices: 1896020--1896107 Score: 149
Period size: 31 Copynumber: 2.8 Consensus size: 31
1896010 TTATATTGTT
*
1896020 AATTAATATTTTATTTAAAATTCAAGAGTTA
1 AATTAATATTTTATTTAAAATTTAAGAGTTA
*
1896051 AATTAATAATTTATTTAAAATTTAAGAGTTA
1 AATTAATATTTTATTTAAAATTTAAGAGTTA
*
1896082 AATTAATATTTTATCTAAAATTTAAG
1 AATTAATATTTTATTTAAAATTTAAG
1896108 TATCTACTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (31 bp):
AATTAATATTTTATTTAAAATTTAAGAGTTA
Found at i:1896489 original size:17 final size:17
Alignment explanation
Indices: 1896467--1896507 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1896457 AGTAACGGGA
1896467 AGCAACTCAAAGCAAAG
1 AGCAACTCAAAGCAAAG
1896484 AGCAACTCAAAGCAAAG
1 AGCAACTCAAAGCAAAG
*
1896501 ACCAACT
1 AGCAACT
1896508 TTGTTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.51, C:0.27, G:0.15, T:0.07
Consensus pattern (17 bp):
AGCAACTCAAAGCAAAG
Found at i:1900001 original size:13 final size:14
Alignment explanation
Indices: 1899970--1900001 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1899960 AATAAAGAAA
1899970 TATTAAAATTCCAT
1 TATTAAAATTCCAT
1899984 T-TTAAAATT-CAT
1 TATTAAAATTCCAT
1899996 TATTAA
1 TATTAA
1900002 TTCAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 12 0.71
14 1 0.06
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (14 bp):
TATTAAAATTCCAT
Found at i:1906917 original size:22 final size:22
Alignment explanation
Indices: 1906891--1906973 Score: 98
Period size: 23 Copynumber: 3.8 Consensus size: 22
1906881 TTGGTGCAGA
1906891 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
*
1906913 GGGAA-CTGATTCCCCCTTTGAAG
1 GGGAATC-GATACCCCC-TTGAAG
* * *
1906936 GGGAACCGATTCCCCC-TGTAG
1 GGGAATCGATACCCCCTTGAAG
1906957 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
1906974 AGAGGTTATG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
21 19 0.36
22 13 0.25
23 20 0.38
24 1 0.02
ACGTcount: A:0.23, C:0.30, G:0.27, T:0.20
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:1912793 original size:129 final size:130
Alignment explanation
Indices: 1912543--1912794 Score: 319
Period size: 129 Copynumber: 1.9 Consensus size: 130
1912533 AACGAGAAAA
* * * *
1912543 AAAACATTATTGTGTGATGGATTCCTTATCATCCACGGCACCACATCTTCAACTAATCCTTGTTG
1 AAAACATTATTGTGCGATGGATTCCTTATCATCCACGGCACCACATCTTCAACCAACCCTTATTG
* * ** *
1912608 CCCAAACCTAACTATTGCTTGAGGACAAGACTTGACTAATGATGAATCGAAGGGGATGAGTGGAG
66 CCCAAACCCAACTATTGCTTGAGGACAAGACTTGACTAAGGATGAAGAGAAAGGGATGAGTGGAG
* *
1912673 AAAACATTA-TGTGCGATGGATTCCTTATCATTCCA-GGCACCTCGTCTTCAACCAACCCTTATT
1 AAAACATTATTGTGCGATGGATTCCTTATCA-TCCACGGCACCACATCTTCAACCAACCCTTATT
** ** * * *
1912736 GCCTGAACCCAACTATTGCTTGAGGGTAAGGCTTGGCTAAGGATGGAGAGAAAGGGATG
65 GCCCAAACCCAACTATTGCTTGAGGACAAGACTTGACTAAGGATGAAGAGAAAGGGATG
1912795 GGTGAGGGTA
Statistics
Matches: 103, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
129 90 0.87
130 13 0.13
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (130 bp):
AAAACATTATTGTGCGATGGATTCCTTATCATCCACGGCACCACATCTTCAACCAACCCTTATTG
CCCAAACCCAACTATTGCTTGAGGACAAGACTTGACTAAGGATGAAGAGAAAGGGATGAGTGGAG
Found at i:1914791 original size:11 final size:11
Alignment explanation
Indices: 1914775--1914799 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1914765 ATACAATTAT
1914775 TTTATTTTAAA
1 TTTATTTTAAA
1914786 TTTATTTTAAA
1 TTTATTTTAAA
1914797 TTT
1 TTT
1914800 GTTATGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATTTTAAA
Found at i:1915341 original size:154 final size:154
Alignment explanation
Indices: 1915061--1915370 Score: 522
Period size: 155 Copynumber: 2.0 Consensus size: 154
1915051 CAAACACTAA
1915061 AATTTTAAACTTAACTTTTCATAAGCACTTTTTAACAGTACTTTTCACATTGATAACTTATTAAT
1 AATTTTAAACTTAACTTTTCATAAGCACTTTTTAACAGTACTTTTCACATTGATAACTTATTAAT
1915126 TTTTATAAATTAATTTTTTCAACTGATAATCAAACACATCATAGTCTAAAAATTTATAAACA-TT
66 TTTTATAAATTAATTTTTTCAACTGATAA-CAAACACATCATAGTCTAAAAATTTATAAACATTT
1915190 AAATTGAATTTTTAGTATGGATATC
130 AAATTGAATTTTTAGTATGGATATC
1915215 AATTTTAAACTTAAC-TTTCATAAGCACTTTTTAACA-TACTTTTCACATTGATAAAAACTTATT
1 AATTTTAAACTTAACTTTTCATAAGCACTTTTTAACAGTACTTTTCACATTGAT---AACTTATT
*
1915278 AATTTTTATAAATTAA-TTTTTCAAACTGATCA-AAACACATCAGTAGTCTAAAAATTTATAAAC
63 AATTTTTATAAATTAATTTTTTC-AACTGATAACAAACACATCA-TAGTCTAAAAATTTATAAAC
1915341 ATTTAAATTGAATTTTTAGTATGGATATC
126 ATTTAAATTGAATTTTTAGTATGGATATC
1915370 A
1 A
1915371 TATCAATAAG
Statistics
Matches: 149, Mismatches: 1, Indels: 11
0.93 0.01 0.07
Matches are distributed among these distances:
152 16 0.11
153 31 0.21
154 42 0.28
155 60 0.40
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (154 bp):
AATTTTAAACTTAACTTTTCATAAGCACTTTTTAACAGTACTTTTCACATTGATAACTTATTAAT
TTTTATAAATTAATTTTTTCAACTGATAACAAACACATCATAGTCTAAAAATTTATAAACATTTA
AATTGAATTTTTAGTATGGATATC
Found at i:1921716 original size:12 final size:12
Alignment explanation
Indices: 1921699--1921726 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1921689 GGCGCTAAGG
1921699 GAAGATTCTACT
1 GAAGATTCTACT
1921711 GAAGATTCTACT
1 GAAGATTCTACT
1921723 GAAG
1 GAAG
1921727 CACAGTTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (12 bp):
GAAGATTCTACT
Found at i:1923173 original size:54 final size:54
Alignment explanation
Indices: 1923056--1923173 Score: 182
Period size: 54 Copynumber: 2.2 Consensus size: 54
1923046 GTTAAATGAC
* * *
1923056 TAGGGGTATAGGTACCCATCAGCCATTCTGTTTTTCTCGGAGCCAAAATTGGCA
1 TAGGGGTATCGATACCCATCAGCCATTCTGTTTTTCTCAGAGCCAAAATTGGCA
** *
1923110 TAGGGGTATCGATACCCATTTGGCATTCTGTTTTTCTCAGAGCCAAAATTGGCA
1 TAGGGGTATCGATACCCATCAGCCATTCTGTTTTTCTCAGAGCCAAAATTGGCA
1923164 TAGGGGTATC
1 TAGGGGTATC
1923174 AGTACACCCT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (54 bp):
TAGGGGTATCGATACCCATCAGCCATTCTGTTTTTCTCAGAGCCAAAATTGGCA
Found at i:1923521 original size:13 final size:13
Alignment explanation
Indices: 1923503--1923539 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
1923493 GATTTTCTTA
1923503 TTGAAAATTATTT
1 TTGAAAATTATTT
*
1923516 TTGAAAATCAATTT
1 TTGAAAAT-TATTT
1923530 TTGAAAATTA
1 TTGAAAATTA
1923540 CTCCCCCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (13 bp):
TTGAAAATTATTT
Found at i:1923838 original size:14 final size:14
Alignment explanation
Indices: 1923819--1923849 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1923809 ATATATAAGC
1923819 ATCTAAGTTCAAGT
1 ATCTAAGTTCAAGT
1923833 ATCTAAGTTCAAGT
1 ATCTAAGTTCAAGT
1923847 ATC
1 ATC
1923850 CAACATCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (14 bp):
ATCTAAGTTCAAGT
Found at i:1925379 original size:20 final size:20
Alignment explanation
Indices: 1925334--1925381 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1925324 TATGTAGTTT
*
1925334 TCAAAACAACATAATTAAAT
1 TCAAAACAACATAATTAAAA
* *
1925354 TAAAAACAACA-ATTTTAAAA
1 TCAAAACAACATA-ATTAAAA
1925374 TCAAAACA
1 TCAAAACA
1925382 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (20 bp):
TCAAAACAACATAATTAAAA
Found at i:1925857 original size:21 final size:19
Alignment explanation
Indices: 1925806--1925928 Score: 111
Period size: 21 Copynumber: 5.8 Consensus size: 19
1925796 GTACCCTTAT
*
1925806 AGGGGTATCGATACACATTCAA
1 AGGGGTATCGATAC-C-TT-GA
1925828 AGAGGGTATCGATACACGTTGA
1 AG-GGGTATCGATAC-C-TTGA
*
1925850 AGGGGTATCGATACCTAGTA
1 AGGGGTATCGATACCTTG-A
*
1925870 AGGGGGTATCGATACCTAGTA
1 A-GGGGTATCGATACCTTG-A
1925891 AGGGGTTATCGATACCTATGA
1 AGGGG-TATCGATACCT-TGA
1925912 AGGGGGTATCGATACCT
1 A-GGGGTATCGATACCT
1925929 GGTGCACAAA
Statistics
Matches: 91, Mismatches: 4, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.02
20 7 0.08
21 56 0.62
22 10 0.11
23 16 0.18
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (19 bp):
AGGGGTATCGATACCTTGA
Found at i:1925901 original size:42 final size:40
Alignment explanation
Indices: 1925831--1925928 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 40
1925821 CATTCAAAGA
*
1925831 GGGTATCGATACACGTTGAAGGGGTATCGATACCTA-GTAAGG
1 GGGTATCGATAC-C-TAGAAGGGGTATCGATACCTATG-AAGG
1925873 GGGTATCGATACCTAGTAAGGGGTTATCGATACCTATGAAGG
1 GGGTATCGATACCTAG-AAGGGG-TATCGATACCTATGAAGG
1925915 GGGTATCGATACCT
1 GGGTATCGATACCT
1925929 GGTGCACAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
40 2 0.04
41 7 0.13
42 42 0.81
43 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.26
Consensus pattern (40 bp):
GGGTATCGATACCTAGAAGGGGTATCGATACCTATGAAGG
Found at i:1927790 original size:237 final size:237
Alignment explanation
Indices: 1927374--1927848 Score: 889
Period size: 237 Copynumber: 2.0 Consensus size: 237
1927364 AAACCATTTA
*
1927374 AAAATGTACCTTTAACATCCATATGATATAATTTAAATTCATTAAAACATGCAAATTCTAATAAC
1 AAAATGTACCTTTAACATCCATATGATATAATTTAAATTCATTAAAACATGCAAATGCTAATAAC
1927439 ATTCTTATTGCTTCCATCCTAGCTACAGAAGCGTATGTTTCATCGTAGTCTATGCCCTCTTCTTG
66 ATTCTTATTGCTTCCATCCTAGCTACAGAAGCGTATGTTTCATCGTAGTCTATGCCCTCTTCTTG
1927504 AGTATAGCTTTGAACAACAAGTCTAGCCTTTTTCCTCACTATATTACCACTTTTATCAAACTTAT
131 AGTATAGCTTTGAACAACAAGTCTAGCCTTTTTCCTCACTATATTACCAC-TTTATCAAACTTAT
1927569 TCCTAAACAACCATTTAATACCTACAGTAGATTTATTACTAGG
195 TCCTAAACAACCATTTAATACCTACAGTAGATTTATTACTAGG
*
1927612 AAAATGTACCTTTAACATCCATATGATAT-ATTTAAATTCATTGAAACATGCAAATGCTAATAAC
1 AAAATGTACCTTTAACATCCATATGATATAATTTAAATTCATTAAAACATGCAAATGCTAATAAC
* * *
1927676 ATTCTTATTGCTTTCATCCTAGCTACGGAAGCGTATGTTTCATCGTAGTCTATGCCTTCTTCTTG
66 ATTCTTATTGCTTCCATCCTAGCTACAGAAGCGTATGTTTCATCGTAGTCTATGCCCTCTTCTTG
1927741 AGTATAGCTTTGAACAACAAGTCTAGCCTTTTTCCTCACTATATTACCACTTTATCAAACTTATT
131 AGTATAGCTTTGAACAACAAGTCTAGCCTTTTTCCTCACTATATTACCACTTTATCAAACTTATT
1927806 CCTAAACAACCATTTAATACCTACAGTAGATTTATTACTAGG
196 CCTAAACAACCATTTAATACCTACAGTAGATTTATTACTAGG
1927848 A
1 A
1927849 CTCTCAACTA
Statistics
Matches: 232, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
236 58 0.25
237 145 0.62
238 29 0.12
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (237 bp):
AAAATGTACCTTTAACATCCATATGATATAATTTAAATTCATTAAAACATGCAAATGCTAATAAC
ATTCTTATTGCTTCCATCCTAGCTACAGAAGCGTATGTTTCATCGTAGTCTATGCCCTCTTCTTG
AGTATAGCTTTGAACAACAAGTCTAGCCTTTTTCCTCACTATATTACCACTTTATCAAACTTATT
CCTAAACAACCATTTAATACCTACAGTAGATTTATTACTAGG
Found at i:1933601 original size:53 final size:54
Alignment explanation
Indices: 1933516--1933634 Score: 170
Period size: 53 Copynumber: 2.2 Consensus size: 54
1933506 AAATGACTAA
* * *
1933516 GGGTATCGGTACCTATCAGGCATTATGTTTTTCTCGGAGCCAAAATTGGCATAG
1 GGGTATCGGTACCCATCAGGCATTATGTTTTTCTCAGAGACAAAATTGGCATAG
*
1933570 GGGTATCGGTACCCAT-TGGCATCT-TGTTTTTCTCAGAGACAAAATTGGCATAG
1 GGGTATCGGTACCCATCAGGCAT-TATGTTTTTCTCAGAGACAAAATTGGCATAG
*
1933623 GGGTACCGGTAC
1 GGGTATCGGTAC
1933635 ACCCTATGAG
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
53 43 0.73
54 16 0.27
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (54 bp):
GGGTATCGGTACCCATCAGGCATTATGTTTTTCTCAGAGACAAAATTGGCATAG
Found at i:1933657 original size:22 final size:22
Alignment explanation
Indices: 1933629--1933678 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
1933619 ATAGGGGTAC
1933629 CGGTACACCCTATGAGGAGTAT
1 CGGTACACCCTATGAGGAGTAT
*
1933651 CGGTACACCCTATGAGGGGTAT
1 CGGTACACCCTATGAGGAGTAT
1933673 CGGTAC
1 CGGTAC
1933679 CTCCTTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.22
Consensus pattern (22 bp):
CGGTACACCCTATGAGGAGTAT
Found at i:1936313 original size:21 final size:19
Alignment explanation
Indices: 1936262--1936363 Score: 96
Period size: 21 Copynumber: 4.8 Consensus size: 19
1936252 GTACCCTTAT
*
1936262 AGGGGTATCGATACACATTCAA
1 AGGGGTATCGATAC-C-TT-GA
1936284 AGAGGGTATCGATACACGTTGA
1 AG-GGGTATCGATAC-C-TTGA
*
1936306 AGGGGTATCGATACCTAGCA
1 AGGGGTATCGATACCTTG-A
1936326 AGGGGGTATCGATACCTATGA
1 A-GGGGTATCGATACCT-TGA
1936347 AGGGGGTATCGATACCT
1 A-GGGGTATCGATACCT
1936364 AATGCATAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
19 2 0.03
20 3 0.04
21 45 0.62
22 6 0.08
23 16 0.22
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (19 bp):
AGGGGTATCGATACCTTGA
Found at i:1936364 original size:21 final size:21
Alignment explanation
Indices: 1936287--1936364 Score: 108
Period size: 21 Copynumber: 3.7 Consensus size: 21
1936277 CATTCAAAGA
1936287 GGGTATCGATACACGT-TGAA-G
1 GGGTATCGATAC-C-TATGAAGG
1936308 GGGTATCGATACCTA-GCAAGG
1 GGGTATCGATACCTATG-AAGG
1936329 GGGTATCGATACCTATGAAGG
1 GGGTATCGATACCTATGAAGG
1936350 GGGTATCGATACCTA
1 GGGTATCGATACCTA
1936365 ATGCATAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.04
20 3 0.06
21 47 0.89
22 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (21 bp):
GGGTATCGATACCTATGAAGG
Found at i:1942761 original size:54 final size:54
Alignment explanation
Indices: 1942703--1942818 Score: 180
Period size: 54 Copynumber: 2.1 Consensus size: 54
1942693 GTTAAATGAC
*
1942703 TAGGGGTATCGGTACCCATCAGGCAT-TCTATTTTTCTCGGAGCCAAAATTGGCA
1 TAGGGGTATCGGTACCCATCAGGCATCT-TATTTTTCTCAGAGCCAAAATTGGCA
** *
1942757 TAGGGGTATCGGTACCCATTTGGCATCTTGTTTTTCTCAGAGCCAAAATTGGCA
1 TAGGGGTATCGGTACCCATCAGGCATCTTATTTTTCTCAGAGCCAAAATTGGCA
1942811 TAGGGGTA
1 TAGGGGTA
1942819 CCAATACACC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
54 56 0.98
55 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (54 bp):
TAGGGGTATCGGTACCCATCAGGCATCTTATTTTTCTCAGAGCCAAAATTGGCA
Found at i:1945479 original size:21 final size:19
Alignment explanation
Indices: 1945463--1945524 Score: 70
Period size: 21 Copynumber: 3.1 Consensus size: 19
1945453 TAGATACACG
1945463 TTGAAGGGGTATCGATACC
1 TTGAAGGGGTATCGATACC
* *
1945482 TAGCTAGGGGGTATCGATACC
1 TTG--AAGGGGTATCGATACC
1945503 TATGAAGGGGGTATCGATACC
1 T-TGAA-GGGGTATCGATACC
1945524 T
1 T
1945525 GGTGCACAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 2 0.06
20 1 0.03
21 31 0.89
22 1 0.03
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (19 bp):
TTGAAGGGGTATCGATACC
Found at i:1950957 original size:73 final size:76
Alignment explanation
Indices: 1950868--1951032 Score: 210
Period size: 74 Copynumber: 2.2 Consensus size: 76
1950858 TTAAATGACT
* * *
1950868 AGGGGTATCGGTACCCATAAGGCATTCTG-TTTTTCTCGAAGCCAAAATTAGCATAGGGGTATCA
1 AGGGGTATCGATACCCATAAGACATTCTGTTTTTTATCGAAGCCAAAATTAGCATAGGGGTATCA
*
1950932 G-CACCCTGTG
66 GACACCCTATG
** * * * *
1950942 A-GGGTATCGATACCCATTTGACATTTTGTTTTTTATCGGAGCCAAAATTTGCATAGGGGTATCG
1 AGGGGTATCGATACCCATAAGACATTCTGTTTTTTATCGAAGCCAAAATTAGCATAGGGGTATCA
1951006 GTACACCCTATG
66 G-ACACCCTATG
1951018 AGGGGTATCGATACC
1 AGGGGTATCGATACC
1951033 TCCTTATTTA
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
73 22 0.29
74 33 0.43
76 9 0.12
77 13 0.17
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (76 bp):
AGGGGTATCGATACCCATAAGACATTCTGTTTTTTATCGAAGCCAAAATTAGCATAGGGGTATCA
GACACCCTATG
Found at i:1958695 original size:6 final size:6
Alignment explanation
Indices: 1958686--1958721 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
1958676 ACAAATACAT
*
1958686 AGGGAG AGGGAG ATGGAG AGGGAG AGGGAG AGGGAG
1 AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG
1958722 CGAGGAACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.64, T:0.03
Consensus pattern (6 bp):
AGGGAG
Found at i:1963145 original size:59 final size:59
Alignment explanation
Indices: 1963016--1963185 Score: 184
Period size: 59 Copynumber: 2.8 Consensus size: 59
1963006 ATGCTTATTG
* *
1963016 TTAGGGATGAAATTGAAATGTTTAAAAAGTTTG-GTGACCAATTTAGAATGAAGGTCCTAGT
1 TTAGGGATGAAATTGAAATATTTAAAAA-TTTGAG-GACTAATTTAGAATGAA-GTCCTAGT
* * *
1963077 TTTGAGATGAAATTGAAATATTCAAAAATTTGAGGA-TAATTTAGAATGATA-TCCATAGT
1 TTAGGGATGAAATTGAAATATTTAAAAATTTGAGGACTAATTTAGAATGA-AGTCC-TAGT
** * * *
1963136 TTAGGGATGAAATCAAAATATTTAAAAGTTTAAGGACTAATTTAAAATGA
1 TTAGGGATGAAATTGAAATATTTAAAAATTTGAGGACTAATTTAGAATGA
1963186 GGATCATATT
Statistics
Matches: 92, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
58 3 0.03
59 45 0.49
60 19 0.21
61 25 0.27
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.34
Consensus pattern (59 bp):
TTAGGGATGAAATTGAAATATTTAAAAATTTGAGGACTAATTTAGAATGAAGTCCTAGT
Found at i:1974168 original size:21 final size:22
Alignment explanation
Indices: 1974133--1974174 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1974123 GACCAACATT
*
1974133 TTTGCATTCTTGCATTCGCATC
1 TTTGCATTCTTGCATTAGCATC
1974155 TTTGCATT-TTGCATTAGCAT
1 TTTGCATTCTTGCATTAGCAT
1974175 TTCACTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.48
Consensus pattern (22 bp):
TTTGCATTCTTGCATTAGCATC
Found at i:1976657 original size:36 final size:36
Alignment explanation
Indices: 1976590--1976697 Score: 121
Period size: 36 Copynumber: 3.0 Consensus size: 36
1976580 TCTCTTGAGG
**
1976590 TTCGTCTCGCTCA-AGACGAGTTTTCCCAAAAACAAAT
1 TTCGTCTCGCT-AGAGAC-AGTTTTCTTAAAAACAAAT
* *
1976627 TTTGTCTCGCTTGAGACAGTTTTCTTAAAAACAAAT
1 TTCGTCTCGCTAGAGACAGTTTTCTTAAAAACAAAT
* *
1976663 TTCGTCTCGCTAGAGATAATTTTCCTT-AAAACAAA
1 TTCGTCTCGCTAGAGACAGTTTT-CTTAAAAACAAA
1976698 ATTAATTATT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
36 44 0.72
37 17 0.28
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.33
Consensus pattern (36 bp):
TTCGTCTCGCTAGAGACAGTTTTCTTAAAAACAAAT
Found at i:1976865 original size:65 final size:65
Alignment explanation
Indices: 1976794--1976922 Score: 197
Period size: 65 Copynumber: 2.0 Consensus size: 65
1976784 AACAAAATTG
* * * *
1976794 ATAAACTTTGAGATTG-TTTCTCTTGAAATAAATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAA
1 ATAAACTTTGAGAATGTTTTC-CTTAAAACAAATTTTGTCTCCCTTAAGACAGTTTCCCTTGAAA
1976858 A
65 A
*
1976859 ATAAACTTTGAGAATGTTTTCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAA
1 ATAAACTTTGAGAATGTTTTCCTTAAAACAAATTTTGTCTCCCTTAAGACAGTTTCCCTTGAAA
1976923 CAAATTTTGT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 54 0.93
66 4 0.07
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (65 bp):
ATAAACTTTGAGAATGTTTTCCTTAAAACAAATTTTGTCTCCCTTAAGACAGTTTCCCTTGAAAA
Found at i:1976903 original size:21 final size:21
Alignment explanation
Indices: 1976879--1976962 Score: 99
Period size: 21 Copynumber: 4.3 Consensus size: 21
1976869 AGAATGTTTT
*
1976879 CCTTAAAACAAATTTTGTCTC
1 CCTTGAAACAAATTTTGTCTC
* *
1976900 CCTTGAGAC--A-GTT-T--C
1 CCTTGAAACAAATTTTGTCTC
1976915 CCTTGAAACAAATTTTGTCTC
1 CCTTGAAACAAATTTTGTCTC
1976936 CCTTGAAACAAATTTTGTCTC
1 CCTTGAAACAAATTTTGTCTC
1976957 CCTTGA
1 CCTTGA
1976963 GATAGTTTCC
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
15 9 0.17
17 2 0.04
18 4 0.08
19 2 0.04
21 35 0.67
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (21 bp):
CCTTGAAACAAATTTTGTCTC
Found at i:1976924 original size:36 final size:36
Alignment explanation
Indices: 1976866--1976941 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
1976856 AAAATAAACT
*
1976866 TTGAGAATGTTTTCCTTAAAACAAATTTTGTCTCCC
1 TTGAGAATGTTTCCCTTAAAACAAATTTTGTCTCCC
*
1976902 TTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCCC
1 TTGAGA-ATGTTTCCCTTAAAACAAATTTTGTCTCCC
1976938 TTGA
1 TTGA
1976942 AACAAATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 36 0.97
37 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
TTGAGAATGTTTCCCTTAAAACAAATTTTGTCTCCC
Found at i:1976974 original size:36 final size:36
Alignment explanation
Indices: 1976934--1977052 Score: 166
Period size: 36 Copynumber: 3.2 Consensus size: 36
1976924 AAATTTTGTC
1976934 TCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTT
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTT
* * * *
1976970 TCCCTCGAAATAAAAGATTTTATCTCCCTTGAGACAGTT
1 TCCCTTG-AA-ACAA-ATTTTGTCTCCCTTGAGATAGTT
*
1977009 TCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTC
1 TCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTT
1977045 TCCCTTGA
1 TCCCTTGA
1977053 GACAGTTTTC
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
36 34 0.48
37 5 0.07
38 5 0.07
39 27 0.38
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.36
Consensus pattern (36 bp):
TCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTT
Found at i:1977090 original size:90 final size:90
Alignment explanation
Indices: 1976890--1977139 Score: 383
Period size: 90 Copynumber: 2.7 Consensus size: 90
1976880 CTTAAAACAA
* *
1976890 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAAACAAATTTTGTC
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTG----AGA--TAGTC
*
1976955 TCCCTTGAGATAGTTTCCCTCGAAATAAAAG
60 TCCCTTGAGACAGTTTCCCTCGAAATAAAAG
*
1976986 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTCTCCCTT
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTCTCCCTT
*
1977051 GAGACAGTTTTCCTCGAAATAAAAG
66 GAGACAGTTTCCCTCGAAATAAAAG
* *
1977076 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCT
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTCTCCCT
1977140 CGAAATAAAT
Statistics
Matches: 146, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
90 94 0.64
92 2 0.01
96 50 0.34
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (90 bp):
ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTCTCCCTT
GAGACAGTTTCCCTCGAAATAAAAG
Found at i:1977093 original size:54 final size:51
Alignment explanation
Indices: 1976992--1977106 Score: 158
Period size: 54 Copynumber: 2.2 Consensus size: 51
1976982 AAAGATTTTA
* * *
1976992 TCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAG
1 TCTCCCTTGAGACAGTTTCCCTCGAAAAAAATTTTGTCTCCCTTGAGACAG
*
1977043 TCTCCCTTGAGACAGTTTTCCTCGAAATAAAAGATTTTGTCTCCCTTGAGACAG
1 TCTCCCTTGAGACAGTTTCCCTCG-AA-AAAA-ATTTTGTCTCCCTTGAGACAG
*
1977097 TTTCCCTTGA
1 TCTCCCTTGA
1977107 AACAAATTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
51 22 0.39
52 2 0.04
53 3 0.05
54 29 0.52
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (51 bp):
TCTCCCTTGAGACAGTTTCCCTCGAAAAAAATTTTGTCTCCCTTGAGACAG
Found at i:1977123 original size:36 final size:36
Alignment explanation
Indices: 1977042--1977634 Score: 648
Period size: 36 Copynumber: 15.9 Consensus size: 36
1977032 CCTTGAGATA
* * *
1977042 GTCTCCCTTGAGACAGTTTTCCTCGAAATAAAAGATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTG-AA-ACAA-ATTTT
1977081 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
* *
1977117 GTCTCCCTTGAGACAGTTTCCCTCGAAATAAATGATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAA-CAA--ATTTT
1977156 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
1977192 GTCT-CCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
*
1977227 GTCTCCCTTGAGACAGTCTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
* *
1977263 GTCTCCCTTGAGACAATTTCCCTTGAAACAAATTTA
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
* *
1977299 GTTTCCCTTAAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
* * *
1977335 GTCTCCCTTGAGATAGTTTCCCTTAAAACAAATTTA
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
1977371 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
* * *
1977407 GTCTCCTTTGAGATAGTTTCCCTCGAAACAGAATAATTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACA-AAT--TTT
* * * *
1977446 GTCTCGCTTGAGATAGTTTCACTTGAAATAAAAGATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTG-AA-ACAA-ATTTT
* ** * * *
1977485 ATCTTGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAAC--AA-ATTTT
* * * *
1977524 GTCTCGCTTGAGATAGTTTCCTTTGAAACAAAAGATCTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAAC--AA-ATTTT
* * *
1977563 GTCTCGCTTGAGATAGTTTCCCTCGAAACAGAATATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAAC--AA-ATTTT
* * * * *
1977602 ATCTCACTTGAGATAGTTTCTCTCGAAACAAAT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
1977635 GATTTTATAA
Statistics
Matches: 492, Mismatches: 50, Indels: 27
0.86 0.09 0.05
Matches are distributed among these distances:
35 35 0.07
36 229 0.47
37 11 0.02
38 6 0.01
39 204 0.41
40 3 0.01
41 4 0.01
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (36 bp):
GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
Found at i:1977179 original size:15 final size:15
Alignment explanation
Indices: 1977159--1977216 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
1977149 TGATTTTGTC
1977159 TCCCTTGAGACAGTT
1 TCCCTTGAGACAGTT
* *
1977174 TCCCTTGAAACAAATTTT
1 TCCCTTGAGAC--A-GTT
1977192 GTCTCCTTGAGACAGTT
1 -TC-CCTTGAGACAGTT
1977209 TCCCTTGA
1 TCCCTTGA
1977217 AACAAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
15 16 0.47
16 2 0.06
17 3 0.09
18 3 0.09
19 2 0.06
20 8 0.24
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (15 bp):
TCCCTTGAGACAGTT
Found at i:1977235 original size:21 final size:21
Alignment explanation
Indices: 1977209--1977345 Score: 87
Period size: 21 Copynumber: 7.4 Consensus size: 21
1977199 TGAGACAGTT
1977209 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
*
1977230 TCCCTTGAGAC--A----GTC
1 TCCCTTGAAACAAATTTTGTC
1977245 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
*
1977266 TCCCTTGAGAC-AA---T-T-
1 TCCCTTGAAACAAATTTTGTC
* *
1977281 TCCCTTGAAACAAATTTAGTT
1 TCCCTTGAAACAAATTTTGTC
*
1977302 TCCCTT-AAGAC--A----GTT
1 TCCCTTGAA-ACAAATTTTGTC
1977317 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
1977338 TCCCTTGA
1 TCCCTTGA
1977346 GATAGTTTCC
Statistics
Matches: 90, Mismatches: 6, Indels: 40
0.66 0.04 0.29
Matches are distributed among these distances:
15 34 0.38
16 5 0.06
17 3 0.03
19 2 0.02
20 5 0.06
21 41 0.46
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.36
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:1984992 original size:20 final size:20
Alignment explanation
Indices: 1984969--1985020 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1984959 AACGCGATCC
1984969 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1984989 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1985009 CCAAAATCGCAA
1 CCAGAATCGCAA
1985021 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:1985101 original size:20 final size:20
Alignment explanation
Indices: 1985076--1985269 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
1985066 GATTTTCCAT
* *
1985076 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
1985096 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
1985116 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1985136 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
1985156 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
1985176 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1985196 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
1985216 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
1985237 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
1985257 AATCGCAACGCGA
1 AATCGCAACGCGA
1985270 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:1985121 original size:40 final size:39
Alignment explanation
Indices: 1985072--1985269 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
1985062 TTGCGATTTT
* ** *
1985072 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
1985110 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
1985151 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
1985191 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
1985230 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1985270 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:1985159 original size:60 final size:60
Alignment explanation
Indices: 1985076--1985268 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1985066 GATTTTCCAT
* ** * *
1985076 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
1985136 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
1985196 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
1985257 AATCGCAACGCG
1 AATCGCAACGCG
1985269 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:1985689 original size:33 final size:33
Alignment explanation
Indices: 1985650--1985720 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1985640 TTCACTTAGA
*
1985650 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1985683 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1985716 TTTCA
1 TTTCA
1985721 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1985860 original size:14 final size:14
Alignment explanation
Indices: 1985841--1985895 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1985831 AGAATGACTG
1985841 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
1985855 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
1985874 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1985888 TCGCAACG
1 TCGCAACG
1985896 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1985878 original size:33 final size:33
Alignment explanation
Indices: 1985841--1985911 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1985831 AGAATGACTG
**
1985841 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1985874 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1985907 TCGCA
1 TCGCA
1985912 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:1985929 original size:19 final size:19
Alignment explanation
Indices: 1985907--1986004 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1985897 GAAACCAAAA
*
1985907 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1985926 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1985940 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1985959 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1985973 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1985992 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1986005 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1985948 original size:14 final size:14
Alignment explanation
Indices: 1985929--1986018 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1985919 TTTCATTTCG
1985929 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1985943 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1985962 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1985976 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1985993 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1986009 CGTTGCGATT
1 CGTTGCGATT
1986019 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1985954 original size:33 final size:33
Alignment explanation
Indices: 1985912--1986026 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1985902 CAAAATCGCA
1985912 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1985945 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1985978 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1986011 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1986027 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Done.